methylKit unite chromosome by chromosome

uniteByChr.R

subsetByChr<-function(methylRawList.obj,my.chr="chr21"){
  
  sub=lapply(methylRawList.obj, function(x) x[x$chr==my.chr]  )
  
 new("methylRawList",sub,treatment=methylRawList.obj@treatment)
  
  
}

my.chrs= unique(methylRawList.obj[[1]]$chr)

result=data.frame()
for(my.chr in my.chrs){
  
  my.subset=subsetByChr(methylRawList.obj,my.chr)
  result=rbind(result, getData(unite(my.subset)))
}

obj=new("methylBase",result,sample.ids=sapply(methylRawList.obj,function(x) [email protected] ),
        assembly="mm9",context="CpG",
        treatment=methylRawList.obj@treatment,
        coverage.index=seq(5,by=3,length.out=length(methylRawList.obj@treatment)),
        numCs.index=seq(5,by=3,length.out=length(methylRawList.obj@treatment)) +1 ,
        numTs.index=seq(5,by=3,length.out=length(methylRawList.obj@treatment)) +2,
        destranded=FALSE,resolution="base" )